Mesquite: A modular system for evolutionary analysis
Mesquite is modular, extendible software for evolutionar...phasis is on phylogenetic analysis, but some of its modules concern population genetics,...it is modular, the analyses available depend on the modules installed. https://github.co...2244 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quanti...2161 days ago
RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
RestrictionDigest can simulate the reference genome digestion and generate comprehensive information of the simulation. It can simulate single-enzyme digestion, double-...2152 days ago
TULIP - The Uncorrected Long read Integration Pipeline
TULIP currently consists of two Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional components and/or implementations are lik...2181 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing...se pairs of each such structural feature. The bpRNA code is written in perl and requires the Graph perl mo...2173 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl....2136 days ago
Nanopolis: polish a genome assembly
Software package for signal-level analysis of Oxford Nanopore sequencing data. Nano...ll SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below). Quickstart http://...2109 days ago
2097 days ago
FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
Here is the command to run the tool: python finisherSC.py destinedFolder mummerPath...r raw_reads.fasta using the following command. perl -pe 's/>[^\$]*$/">Seg"...sta cp newRaw_reads.fasta raw_reads.fasta perl -p...2084 days ago
Synima: a Synteny imaging tool for annotated genome assemblies
Synima written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outpu...2013 days ago